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Forum: Illumina/Solexa 07-17-2017, 06:09 PM
Replies: 3
Views: 1,723
Posted By JVGen
I just took the index sequence and converted to...

I just took the index sequence and converted to moles/volume (molarity). Dust off your old pal Avogadro.
Forum: Illumina/Solexa 03-23-2017, 08:11 AM
Replies: 0
Views: 493
Posted By JVGen
Amplicon Sequencing with Nextera Prep & MiniSeq: Tandem Repeats?

Hi Everyone,

I'm sequencing PCR amplicons generated from gDNA (HIV proviruses). I've noticed something unusual that appears in a handful of the samples I've sequenced, even my controls...
Forum: Bioinformatics 03-02-2017, 04:42 AM
Replies: 304
Views: 78,366
Posted By JVGen
Hi Brian, I always mix the placement of the...

Hi Brian,

I always mix the placement of the adapters up. I'm not sure what the location I'm referring to is called, but it is the sequence that is added by the transposase, and the location where...
Forum: Bioinformatics 03-01-2017, 04:25 AM
Replies: 304
Views: 78,366
Posted By JVGen
Thanks Brian. It doesn't look like clumpify has...

Thanks Brian. It doesn't look like clumpify has been built into Geneious as of yet, so I'll have to skip that trimming step.

Also, I was wondering why there were 71 sequences in the Nextera...
Forum: Bioinformatics 02-28-2017, 05:15 AM
Replies: 94
Views: 19,603
Posted By JVGen
Hi Brian, I'm running into a problem where...

Hi Brian,

I'm running into a problem where Tadpole is creating two contigs, yet the generated contigs have identical overlapping ends. I've shared the FASTA files and reads via Google Drive. The...
Forum: Bioinformatics 02-28-2017, 03:18 AM
Replies: 304
Views: 78,366
Posted By JVGen
Thanks Brian. If I intend to merge reads...

Thanks Brian.

If I intend to merge reads using BBMerge, should I only Adapter Trim, Merge, and then Trim with the other parameters?

I'm hoping to use "mix=t" with BBMerge, if downstream...
Forum: Bioinformatics 02-27-2017, 08:31 AM
Replies: 304
Views: 78,366
Posted By JVGen
Hi Brian, Thanks for the explanation. In...

Hi Brian,

Thanks for the explanation. In general, I have pretty high coverage which is why I had the trimming parameters set so strict - a minimum of ~1000x coverage in 150 x 2 PE reads (I'm...
Forum: Bioinformatics 02-26-2017, 11:15 AM
Replies: 304
Views: 78,366
Posted By JVGen
Hi Brian, I started using an HPC (36 CPUs @...

Hi Brian,

I started using an HPC (36 CPUs @ 3.5 GHz each & 60 GB RAM) to processes NGS data. I noticed that while using BBDuk, neither the RAM nor processors are being challenged, yet BBDuk takes...
Forum: Illumina/Solexa 02-10-2017, 11:37 AM
Replies: 3
Views: 1,723
Posted By JVGen
Nextera XT v2 Index - Oligo Concentrations?

I use Nextera XT v2 Indexes for library prep, but I can't stand the tubes that Illumina provides them in. I'm thinking of ordering from a third party in a plate format, and dispensing into strip...
Forum: Bioinformatics 02-03-2017, 08:03 AM
Replies: 94
Views: 19,603
Posted By JVGen
Hi Brian, I was wondering if there was a way...

Hi Brian,

I was wondering if there was a way to save the reads that are used during contig assembly, so that they can be mapped back to the generated consensus in a downstream step. I noticed the...
Forum: Bioinformatics 01-17-2017, 02:46 PM
Replies: 94
Views: 19,603
Posted By JVGen
Thank you for the input, Brian. I tried bm1=8...

Thank you for the input, Brian. I tried bm1=8 bm2=2 earlier, as per info available on JGI's website. It unfortunately still splits, though I haven't tried bm1=6 yet. Of course, this is an instance...
Forum: Bioinformatics 01-17-2017, 12:58 PM
Replies: 94
Views: 19,603
Posted By JVGen
Hi Brian, Reads are 150x2, and I generally...

Hi Brian,

Reads are 150x2, and I generally have >100x coverage. I tried increasing to k=60, but that splits the input into many more contigs.

My goal here is to extract a consensus sequence...
Forum: Bioinformatics 01-17-2017, 11:52 AM
Replies: 94
Views: 19,603
Posted By JVGen
Hi Brian, I'm getting an error while trying...

Hi Brian,

I'm getting an error while trying to use tadpole. Tadpole.sh brings up the expected list of options, so I know that I've directed the terminal correctly.

However, adding the...
Forum: Bioinformatics 01-06-2017, 06:28 AM
Replies: 639
Views: 126,729
Posted By JVGen
I think I might try something like window = 15...

I think I might try something like window = 15 and entropy 0.01. That should get rid of the mononucleotide strings. The HIV genome generally doesn't have anything like that, so it should work.

...
Forum: Bioinformatics 01-05-2017, 01:13 PM
Replies: 639
Views: 126,729
Posted By JVGen
Hi Brian, That's unfortunately about as much...

Hi Brian,

That's unfortunately about as much as the error messages says - that Tadpole cannot use a mixture of paired and unpaired reads. It might be the read-name format that is throwing it off?...
Forum: Bioinformatics 01-05-2017, 12:05 PM
Replies: 639
Views: 126,729
Posted By JVGen
Save Reads for Tadpole

Hi Brian, Geno,

I'm wondering if it's possible to save the reads that BBMap uses in its assembly, for subsequent use with Tadpole?

I have some junk reads that I think might be interfering with...
Forum: Bioinformatics 12-06-2016, 04:13 AM
Replies: 212
Views: 54,023
Posted By JVGen
Hi Brian, that's Geneious I'm viewing in. I...

Hi Brian, that's Geneious I'm viewing in. I download and tried using IGV, but I get an error when trying to load up the SAM file. I shared the SAM file with you on google drive. I included the...
Forum: Bioinformatics 12-05-2016, 05:14 PM
Replies: 212
Views: 54,023
Posted By JVGen
Hi GenoMax, The entirety of my reference is...

Hi GenoMax,

The entirety of my reference is only 9000 bp, so I think the default maxindel size is appropriate. What does intronlen do?

Thanks!
JV
Forum: Bioinformatics 12-05-2016, 02:59 PM
Replies: 212
Views: 54,023
Posted By JVGen
Hi Brian, I am trying to use BBMap to align...

Hi Brian,

I am trying to use BBMap to align 150 bp paired end reads to a 10 kb reference. The reference is an HIV genome, and my sequencing input is PCR amplified HIV proviruses (means I get lots...
Forum: Illumina/Solexa 11-11-2016, 02:37 PM
Replies: 7
Views: 3,897
Posted By JVGen
Thanks SNP. You use the indexes interchangeably?...

Thanks SNP. You use the indexes interchangeably? No alterations? Just treat the XT indexes as the standard Nextera indexes?

Thanks much!
Forum: Illumina/Solexa 11-11-2016, 12:39 PM
Replies: 7
Views: 3,897
Posted By JVGen
Nuc, can you provide anymore information on using...

Nuc, can you provide anymore information on using the Nextera XT indexes with the Nextera protocol? We're about to purchase a MiniSeq with the intention of running the reduced-volume reactions for...
Forum: Bioinformatics 11-07-2016, 11:02 AM
Replies: 304
Views: 78,366
Posted By JVGen
Hi Brian, You are correct. While the file...

Hi Brian,

You are correct. While the file names were correct in the program interface, upon export the "_" were introduced. I apologize for not opening up the fastq file in a texteditor to be...
Forum: Bioinformatics 11-07-2016, 10:32 AM
Replies: 304
Views: 78,366
Posted By JVGen
Hi Brian, I just recently started using...

Hi Brian,

I just recently started using BBDuk to adapter and quality trim. I then use the reads to assemble in Spades, but ran into an issue. The error correction software that Spades uses...
Forum: Bioinformatics 11-04-2016, 09:39 AM
Replies: 3
Views: 1,110
Posted By JVGen
Thank you! And such a prompt response = A+

Thank you! And such a prompt response = A+
Forum: Bioinformatics 11-04-2016, 09:27 AM
Replies: 3
Views: 1,110
Posted By JVGen
I won't be much help, but I'm getting the same...

I won't be much help, but I'm getting the same error. I'll let you know if I find a fix. In the meantime, why don't we both contact the Spades folks: [email protected]
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